transeq frame list

[Peter Rice]

"Gary Williams, Tel 01223 494522" wrote:
>
> David.Bauer at SCHERING.DE wrote:
> >
> > transeq -help says that -frame should be a list.
> > But if I specify -frame=1,2,3 it crashes with segmentation fault
> > and no visible error in the debug file.
> > The last message there is that it correctly recognised the frame list.
> > It seems frame can only be a character.
> > In fact it is OK because there is the F as alias for 1,2,3
> > but -help should give the correct type.
> 
> I have changed transeq's '-frame' qualifier so that it can take one or
> more frame values:

OK. I tested it. -frame=1,2,3 gives the same results as -frame=f

> David has also suggested a change of the name of ACD type 'list'
> to be 'menu'.
>
> This would break lots of parsers, but perhaps we could keep the
> ACD type 'list' in the .acd files, but the name 'list' could be
> changed to be 'menu' when displaying -help?

Done. Lists will say 'menu list' in messages, and 'menu' in the help
output. Selects will say 'selection list'.

Also, the error message for a bad list or select option will include the
valid options (for lists this is the short code). For example:

% transeq tembl:paamir -frame=4
Translate nucleic acid sequences
Error: '4' is not a valid menu option
Accepted short codes are: 1,2,3,F,-1,-2,-3,R,6
Error: Bad menu option '4'

The list and select options must be in a comma-separated list
(-frame=1,2,3). White space was allowed up to now (-frame="1 2 3"), but I
think is rarely used (it is easy to turn on again). Now you can use:

% transeq -frame="Forward three frames"

... which is the long name for 'F' in the ACD file. Users never see these
unless they are prompted for a required/optional value, as for example in
msbar which has 3 prompted lists (menus).

The list/menu and message changes are all in ajax/ajacd.c ... which can be
added to the patchfiles although I suspect we are close to a new release
anyway.

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723